{ "type": "genome", "identifier": "GCF_023283845.1", "organism": "Shewanella marinintestina", "title": "Shewanella marinintestina", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Karolinska Institutet", "publication": [ {} ], "properties": { "assembly_accession": "GCF_023283845.1", "bioproject": "PRJNA224116", "biosample": "SAMN24537876", "wgs_master": "JAKILC000000000.1", "refseq_category": "reference genome", "taxid": "190305", "species_taxid": "190305", "organism_name": "Shewanella marinintestina", "infraspecific_name": "strain=LMG 21403", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/05/09", "asm_name": "ASM2328384v1", "asm_submitter": "Karolinska Institutet", "gbrs_paired_asm": "GCA_023283845.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/023/283/845/GCF_023283845.1_ASM2328384v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4879403", "genome_size_ungapped": "4879403", "gc_percent": "42.500000", "replicon_count": "0", "scaffold_count": "48", "contig_count": "48", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_023283845.1-RS_2024_05_18", "annotation_date": "2024-05-18", "total_gene_count": "4276", "protein_coding_gene_count": "4119", "non_coding_gene_count": "136", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-05-09", "dateModified": "2022-05-09", "datePublished": "2022-05-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Shewanella marinintestina" ], "sample_taxid": [ "190305" ], "sample_host_organism": [ "squid" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "1.390 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4879403", "Number of Sequences": "48", "Longest Sequences (bp)": "529997", "N50 (bp)": "221610", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.6", "Number of CDSs": "4140", "Average Protein Length": "331.0", "Coding Ratio (%)": "84.3", "Number of rRNAs": "2", "Number of tRNAs": "110", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shewanella marinintestina", "strain": "strain=LMG 21403", "accession": "GCA_023283845.1", "taxid": 190305, "species_taxid": 190305, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1597, "total_fragments": 1599, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Shewanella sairae", "strain": "strain=JCM 11563", "accession": "GCA_019655015.1", "taxid": 190310, "species_taxid": 190310, "relation_to_type": "type", "validated": true, "ani": 88.0402, "matched_fragments": 1201, "total_fragments": 1599, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella sairae", "strain": "strain=LMG 21408", "accession": "GCA_023283535.1", "taxid": 190310, "species_taxid": 190310, "relation_to_type": "type", "validated": true, "ani": 88.0205, "matched_fragments": 1205, "total_fragments": 1599, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella pealeana", "strain": "strain=ATCC 700345", "accession": "GCA_000018285.1", "taxid": 70864, "species_taxid": 70864, "relation_to_type": "type", "validated": true, "ani": 82.8296, "matched_fragments": 990, "total_fragments": 1599, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella fidelis", "strain": "strain=ATCC BAA-318", "accession": "GCA_000518605.1", "taxid": 173509, "species_taxid": 173509, "relation_to_type": "type", "validated": true, "ani": 82.6078, "matched_fragments": 1061, "total_fragments": 1599, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella halifaxensis", "strain": "strain=HAW-EB4", "accession": "GCA_000019185.1", "taxid": 271098, "species_taxid": 271098, "relation_to_type": "type", "validated": true, "ani": 82.1076, "matched_fragments": 972, "total_fragments": 1599, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella schlegeliana", "strain": "strain=JCM 11561", "accession": "GCA_016765635.1", "taxid": 190308, "species_taxid": 190308, "relation_to_type": "type", "validated": true, "ani": 82.1066, "matched_fragments": 944, "total_fragments": 1599, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella schlegeliana", "strain": "strain=LMG 21406", "accession": "GCA_023283605.1", "taxid": 190308, "species_taxid": 190308, "relation_to_type": "type", "validated": true, "ani": 81.9799, "matched_fragments": 961, "total_fragments": 1599, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella gelidimarina", "strain": "strain=ATCC 700752", "accession": "GCA_023283945.1", "taxid": 56813, "species_taxid": 56813, "relation_to_type": "type", "validated": true, "ani": 79.6392, "matched_fragments": 612, "total_fragments": 1599, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella abyssi", "strain": "strain=DSM 17171", "accession": "GCA_023284025.1", "taxid": 311789, "species_taxid": 311789, "relation_to_type": "type", "validated": true, "ani": 79.5954, "matched_fragments": 604, "total_fragments": 1599, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 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"s__Shewanella piezotolerans", "ani": 80.0397, "matched_fragments": 653, "total_fragments": 1599, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_016757755.1", "gtdb_species": "s__Shewanella sp016757755", "ani": 79.6822, "matched_fragments": 631, "total_fragments": 1599, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_002836205.1", "gtdb_species": "s__Shewanella sp002836205", "ani": 79.6143, "matched_fragments": 653, "total_fragments": 1599, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.46", "min_intra_species_ani": "99.13", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003605125.1", "gtdb_species": "s__Shewanella algidipiscicola", "ani": 78.6409, "matched_fragments": 321, "total_fragments": 1599, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "98.64", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007567505.1", "gtdb_species": "s__Shewanella donghaensis", "ani": 77.7816, "matched_fragments": 305, "total_fragments": 1599, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.227, "cell_length": 0.265, "doubling_h": 0.077, "growth_tmp": 25.0, "optimum_tmp": 22.248, "optimum_ph": 7.147, "genome_size": 4868941.65, "gc_content": 46.142, "coding_genes": 4161.776, "rRNA16S_genes": 9.437, "tRNA_genes": 107.731, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.333, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.812, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.187, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Shewanella", "marinintestina" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }